My articles

Yesterday, I was at Rebekah's Bread of Life channel, and asked the atheists, what they would do, if the God of the Bible would prove his existence to them. If they would worship Him, or just acknowledge His existence, and move on with their life as if he would not exist. First, they were questioning how God would do that and ranted about that for minutes. After I finally got them to answer my question, explaining that in my thought experiment, they should simply take it as a fact, that God was capable of doing that, they, hesitating, tried to evade again, asking which God of the Bible, there was Elohim, Jahweh, Elijah, etc. In the end, they admitted: The God of the Bible is evil, a genocidal monster, not worth our worship.
Who seeks with a pure heart, finds. Disbelieving in God's existence has in my view, only in very rare cases something to do with people not finding evidence. It has to do with people rejecting God on other grounds.

We celebrate and worship the Lord, which is our hope and savior.
Atheists have nothing to celebrate nor to worship, or hope for.
We have a positive case that we proclaim,
Atheists only lament and criticize what we believe, and only proclaim what they lack.
We have evidence pointing to the God of the Bible through natural and scriptural theology. They have no evidence that warrants a no-God world.
We have intellectual satisfaction. They have cognitive dissonance.
We look forward to our eternal destiny in heaven. They look forward to the grave.
We know our Lord lives, even if we cannot prove it. They confess ignorance.
We: 1.
Atheists: O.
I see no reason why I should become an atheist.

Extreme genome repair, and remarkable morphogenesis by self-assembly point to design

https://reasonandscience.catsboard.com/t2061p275-my-articles#9626

Extreme Genome Repair (2009): If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal 1

T. Devitt (2014): John R. Battista, a professor of biological sciences at Louisiana State University, showed that E. coli could evolve to resist ionizing radiation by exposing cultures of the bacterium to the highly radioactive isotope cobalt-60. “We blasted the cultures until 99 percent of the bacteria were dead. Then we’d grow up the survivors and blast them again. We did that twenty times,” explains Cox. The result were E. coli capable of enduring as much as four orders of magnitude more ionizing radiation, making them similar to Deinococcus radiodurans, a desert-dwelling bacterium found in the 1950s to be remarkably resistant to radiation. That bacterium is capable of surviving more than one thousand times the radiation dose that would kill a human. 2

Simple bacteria can restart their 'outboard motor' by hotwiring their own genes (2015):
Unable to move and facing starvation, the bacteria evolve a replacement flagellum - a rotating tail-like structure that acts like an outboard motor - by patching together a new genetic switch with borrowed parts. When an organism suffers a life-threatening mutation, it can rapidly rewire its genes. The remarkable speed with which old genes take on new tasks suggests that life has unexpected levels of genetic flexibility.  In theory, the bacteria should have starved to death and effectively gone extinct. Yet over the course of a weekend, they managed to patch themselves back together with borrowed genes." Scientists made the discovery by accident while researching ways to use naturally occurring bacteria to improve the yield of crops. A microbe was engineered so that it could not make its ‘propeller-like' flagellum and forage for food. However, when a researcher accidentally left the immotile strain out on a lab bench, the team discovered the bacteria had evolved over just a few days. The new variety of bacteria had resurrected their flagella in the process.

Remarkably, this happened because the mutants had rewired a cellular switch, which normally controls nitrogen levels in the cell, to activate the flagellum. This rescued these bacteria, which faced certain death if they didn't move to new food sources. The bacteria being studied, Pseudomonas fluorescens, are among a group of bacteria scientists are researching for use in agriculture, as a kind of ‘plant probiotic'. These could help crops grow or fight off diseases, leading to higher yields. However, a key problem is that the bacteria lack resilience, as their positive effects can stop working after only a short period of time. Dr Jackson, a microbiologist at Reading, said: "Plant probiotics could make crops grow more reliably in the future, helping to feed the world's growing population. This new study shows that these bacteria are more resilient than previously thought, as they show a remarkable capacity to overcome catastrophic changes and find a way to survive. "This gives us crucial insights into how bacteria could survive and change, and the challenge now is to see if this occurs in their natural soil and plant environment." 3

K. Eric Drexler: Engines of Creation 2.0 ( 2006): The T4 phage, acts like a spring-loaded syringe and looks like something out of an industrial parts catalog. It can stick to a bacterium, punch a hole, and inject viral DNA (yes, even bacteria suffer infections). Like a conqueror seizing factories to build more tanks, this DNA then directs the cell’s machines to build more viral DNA and syringes. Like all organisms, these viruses exist because they are fairly stable and are good at getting copies of themselves made. Whether in cells or not, nanomachines obey the universal laws of nature. Ordinary chemical bonds hold their atoms together, and ordinary chemical reactions (guided by other nanomachines) assemble them. Protein molecules can even join to form machines without special help, driven only by thermal agitation and chemical forces. By mixing viral proteins (and the DNA they serve) in a test tube, molecular biologists have assembled working T4 viruses. The machinery of the T4 phage, for example, self-assembles from solution, apparently aided by a single enzyme.…self-assembling structures (…For a description of molecular self-assembly, including that of the T4 phage and the ribosome, see Chapter 36 of Lehninger’s  Biochemistry 7)

This ability is surprising: imagine putting automotive parts in a large box, shaking it, and finding an assembled car when you look inside! Yet the T4 virus is but one of many self-assembling structures.  (M. YANAGIDA, 1984: The virus particle contains more than 3,000 protein subunits of some 30 polypeptide species !!) Molecular biologists have taken the machinery of the ribosome apart into over fifty separate protein and RNA molecules, and then combined them in test tubes to form working ribosomes again. To see how this happens, imagine different T4 protein chains floating around in water. Each kind folds up to form a lump with distinctive bumps and hollows, covered by distinctive patterns of oiliness, wetness, and electric charge. Picture them wandering and tumbling, jostled by the thermal vibrations of the surrounding water molecules. From time to time two bounce together, then bounce apart. Sometimes, though, two bounce together and fit, bumps in hollows, with sticky patches matching; they then pull together and stick. In this way protein adds to protein to make sections of the virus, and sections assemble to form the whole.  4

E. V. Koonin, the logic of chance, page 376:  Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery that behaves like this and I personally will build a temple to your name! 5

AlphaFold  (2020)  What a protein does largely depends on its unique 3D structure. Figuring out what shapes proteins fold into is known as the “protein folding problem”, and has stood as a grand challenge in biology for the past 50 years. In a major scientific advance, the latest version of our AI system AlphaFold has been recognized as a solution to this grand challenge by the organizers of the biennial Critical Assessment of protein Structure Prediction (CASP). 6

Comment: Imagine the engineering effort that it would take for protein engineers to produce nanomachines that would need no nano arms and nano hands to assemble complex nanomachines, but design parts that would be able to assemble on their own just by shaking them, like motors, bearings, and moving parts coming together randomly, and then self-assemble into a fully operational nano-machine. The engineers would need to know the single individual forces and how they would interact with the forces from the other parts. The problem becomes even more apparent when we consider that one of the forces that influence proteins is for example Van der Waals forces which operate based on quantum mechanical principles.   R. W. Newberry (2019): The dominant contributors to protein folding include the hydrophobic effect and conventional hydrogen bonding, along with Coulombic interactions and van der Waals interactions. Human technology and advance is far from being able to design this. What a feat would THAT be!

1. Rodrigo S. Galhardo: Extreme Genome Repair 2012 Apr 4.
2. T. Devitt: In the lab, scientists coax E. coli to resist radiation damage March 17, 2014
3. WEEKEND EVOLUTION: BACTERIA 'HOTWIRE THEIR GENES' TO FIX A FAULTY MOTOR 26 February 2015
4. K. Eric Drexler: Engines of Creation 2.0 ( 2006)
5. E. V. Koonin, The logic of chance (2012), page 376
6. AlphaFold: a solution to a 50-year-old grand challenge in biology November 30, 2020
7. https://archive.org/details/biochemistrymole00lehn_0/mode/2up?view=theater&q=biochemistry%2C+lehninger

God is the ultimate, and fundamental being, over all.

He glorifies Himself through those that he saved through Christ's suffering on the cross, giving them loving grace, forgiveness for his sins, and eternal life.

But he also glorifies himself over evildoers and those that deny him.
Because he will display His justice to them.

5 Moses 32.35:  Vengeance is mine, and recompense, for the time when their foot shall slip; for the day of their calamity is at hand, and their doom comes swiftly.’

Justice is only served when unrighteousness is punished accordingly, and righteously. By judging the world at the end of the day, God will display that he is just, that he is light, and no darkness in Him. All evil will come to light and judged, and justice will be established, and God as the holy, governing his creation in righteousness and justice, confirmed.

The result will be:

Philippians 2:10-11 New Century Version (NCV)
so that every knee will bow to the name of Jesus— everyone in heaven, on earth, and under the earth. And everyone will confess that Jesus Christ is Lord and bring glory to God the Father.

That means, all those that will be condemned, will agree that their condemnation is justified and just. They may curse God in their pain in all eternity, but it will not be because they are angry for thinking they were judged in unrighteousness, but because of their pain.

God also displays His power by being the creator of the micro, and the macro. For knowing each atom, each molecule in our body, and knowing each star by name. He knew how to create life, and is lord over every detail of His creation.

The ribosome is analogous to a human-made 3D printer

Vault particles, made by a 3d Polyribosome nano-printer
https://reasonandscience.catsboard.com/t2112-vault-particles-made-by-a-3d-polyribosome-nano-printer

It is the translation machinery in every cell, that translates the message of DNA, and synthesizes proteins, the molecular machines in the cell. It polymerizes amino acids, or joins one to another, forming long amino acid chains, that afterward fold into 3D, to become functional. Each exercises its specific task and function in the cell.

The marvel of the ribosome is, it has a pocket, called the inner core of the peptidyl transferase center. Researchers reported:

" We identified a single functional group with crucial importance for peptide bond catalysis— namely, the ribose 20'-OH at A2451. This ribose 20 group needs to maintain hydrogen donor characteristics in order to promote effective amide bond formation.

My comment: A precise, minutely orchestrated arrangement of just two main players,  the interaction of ribose 2'-OH at position A2451, and the 2’ hydroxyl of the P site substrate A76 is pivotal in orienting substrates in the active site for optimal catalysis, and play a key role in polypeptide bond formation. The ribosome promotes the reaction of the amino acid condensation by properly orienting the reaction substrates. Key in the reaction is the presence of a proton shuttling group.  The observed 100-fold reduction in the reaction rate by mutation of the P-site A76 20-OH group is an indication of this group's activity during the peptidyl transfer reaction.

The positioning of all substrates, transition states, and ribosomal residues contributing to the concerted redistribution of charges must be tightly controlled to achieve efficient transpeptidation. This 2'-OH renders almost full catalytic power. These data highlight the unique functional role of the A2451 2'-OH for peptide bond synthesis among all other functional groups at the ribosomal peptidyl transferase active site.

Protein synthesis is VITAL for all life. If that arrangement was not right from the beginning, no life. How did that state of affairs originate? The peptidyl transferase center is often claimed to be the product of the RNA world since it is not made of proteins using amino acids, but RNA. It has a size of almost 3000 RNAs. How did that form prebiotically, if RNA chains over 40 monomer units break down? If RNA is highly unstable, and ribose, depending on the temperatures, can disintegrate in days, usually in 40 days or so?

I go in-depth into the topic of the prebiotic origin of RNA in my recent book: On the Origin of Life and Virus World by means of an Intelligent Designer: The Factory Maker, Paley's Watchmaker Argument 2.0

https://www.amazon.com/-/pt/dp/B0BJ9RYMD6/ref=sr_1_1?__mk_pt_BR=%C3%85M%C3%85%C5%BD%C3%95%C3%91&crid=1487RO32KGIY&keywords=otangelo%20grasso&qid=1665878930&sprefix=otangelo%20grasso%2Caps%2C271&sr=8-1

He is also Lord over the macro world.

Eric Metaxas: Is atheism dead? page 55
Where We Are in the Universe Before we move from this chapter on the fine-tuning of Earth to our next chapter on the fine-tuning of the entire universe, we should touch on what lies between them. Because the very placement of Earth within the universe is an example of fine-tuning. This is probably even harder for us to comprehend than the idea that Jupiter’s and Saturn’s existence is crucial to our existence. But even the position of our solar system within our galaxy— the Milky Way—is vital to the existence of life here on Earth. Our solar system is located on the inner edge of the Orion Arm of our galaxy, about twenty-six thousand light-years from the center. Science now understands that this is crucial to life on Earth in several ways. If we were closer to the galaxy’s center, the radiation hitting us would be far greater,  because there are many more stars in the galaxy’s center than out here on the spiral arms where we exist. So at the center there are more “active galactic nucleus outbursts” (AGNs), as well as more supernovae and more gamma ray bursts. That would make life here impossible. We would also be far more likely to be hit by comets, which are more numerous. Gonzalez and Richards call where we are in our solar system the “Galactic Habitable Zone,” meaning that it is the ideal location for a planet like ours to form and support life. But if we were farther out from the center, there would be other problems. Stars farther out are orbited by planets significantly smaller than Earth, so as we have said, that would mean no atmosphere capable of supporting life. Neither would they be able to sustain plate tectonics, which is another element absolutely crucial to life as we know it that we will touch on in Chapter Five. The authors even say that our galaxy is better suited for life than 98 percent of the other galaxies near us. For one thing, it is shaped like a spiral. Stars in elliptical galaxies have less-ordered orbits, like bees flying around a hive, so they are more likely to visit their galaxy’s dangerous central regions. They’re also more likely to pass through interstellar clouds at disastrously high speeds. So in many ways our galaxy —a late-type, metal-rich, spiral galaxy with orderly orbits and comparatively little danger between spiral arms—just happens to be that rare galaxy perfectly suited for life, and our placement within that galaxy also happens to be perfectly suited for life. What shall we make of any of this? Science now tells us that all of these varied parameters are not merely helpful for life on Earth, but are inescapably necessary for it? Can we face that our existence looks like nothing less than a mathematical impossibility? It is as though the more clearly we see these things, the more difficult they are to take in.
https://3lib.net/book/18063091/2dbdee

God is glorified by displaying his love, grace, and mercy through Jesus Christ, who did not fear the cross but obeyed the father,  humbly carried it, and permitted it to be nailed on to it like a criminal, naked, and with shame, without having committed any crime or sin.

God is glorified in each YouTube atheist who lies, claiming that there is no evidence for His existence, and calls Him evil, because he judges the world. On judgment day, they will know better, and bow and give Him glory.

God is glorified in His creation. A true master of wisdom, sublime intelligence, and power, far above our comprehension, creating the universe, galaxies, stars, and everything fine-tuned, from the universe to the earth, with creatures of incredible beauty, no human artist comes even close to creating such beauty. Creating atoms with the right laws, sizes, masses, charges, and forces. He created the molecular world, unimagined a hundred years ago, with incredibly ingenious masterfully engineered solutions, arranging atoms and fine-tuning molecules like the nucleobases to permit the right hydrogen bonding to form the Watson Crick ladder, and the DNA information molecule, which is life essential.

God is worthy of worship, glory, praise, and Lordship. You believe? You are beloved and will be rewarded according to your faith. You disbelieve? God will display His glory on you, and one day, you will bow as well.

It's time to take the right decision now. Tomorrow, it could be too late.

How you can get Saved!
https://reasonandscience.catsboard.com/t2501-how-you-can-get-saved

Elaborated Tunnel Architectures in Enzyme Systems point to a designed setup

RNA and DNA belong to the four basic building blocks of life. They are complex macromolecules made of three constituents: the base, the backbone, which is the ribose five-carbon sugar, and phosphate, the moiety which permits DNA polymerization and catenation of monomers, to become polymers. The nucleobases are divided into pyrimidine and purines. These bases must be made in complex biosynthesis pathways in the cell, requiring several molecular machines, and enzymes, that perform the gradual, stepwise operations to yield the nucleobases, which, in the end, are handed over for further processing. Pyrimidines, one of the two classes, require 7 enzymes, of which Carbamoyl phosphate synthase II is the first in the production line. 

In bacteria, a single enzyme supplies carbamoyl phosphate for the synthesis of arginine and pyrimidines. The bacterial enzyme has three separate active sites, spaced along a tunnel nearly 100 Å long. Bacterial carbamoyl phosphate synthetase provides a vivid illustration of the channeling of unstable reaction intermediates between active sites. This reaction consumes two molecules of ATP: One provides a phosphate group and the other energizes the reaction.  The need for this channel exists to efficiently translocate reactive gaseous molecules that can either be toxic to the cell or are reactive intermediates that need to be delivered to complete a coupled reaction.

Comment: Consider that no lifeform exists that does not use DNA and RNA. Therefore, the synthesis of these molecules is a prerequisite for life. The origin of this metabolic pathway can therefore not be explained through evolution. Either it was design or random nonguided fortunate events.  

Tunnel Architectures in Enzyme Systems that Transport Gaseous Substrates

Derinkuyu Underground City in Cappadocia, Turkey, is one of the deepest and most fascinating multilevel subterranean cities, excavated in tunnel systems. Specifically constructed, elaborated Air ducts ensure fresh oxygen supply, and the oxygen ratio inside never changes no matter at what level one is in. Such systems are always engineering marvels, and must be precisely calculated, and constructed. Remarkably, some proteins act similarly and exist in molecular biological systems.  

Ruchi Anand (2021): Tunnels connect the protein surface to the active site or one active site with the others and serve as conduits for the convenient delivery of molecules. Tunnels transferring small molecules such as N2, CH4, C2H6, O2, CO, NH3, H2, C2H2, NO, and CO2 are termed gaseous tunnels. Conduits that have a surface-accessible connection and can accept gases from the surroundings are named external gaseous (EG) tunnels. Whereas, buried gaseous tunnels that do not emerge to the surface are named internal gaseous (IG) tunnels. In some cases, the tunnels can be performed, permanently visible within the protein structure such that the natural breathing motions in proteins do not alter the tunnel dimensions to the extent that the radius of the gaseous tunnel falls below the minimum threshold diameter, e.g., carbamoyl phosphate synthetase (CPS) has a preformed tunnel. In contrast, it can be transient such that the tunnel diameter is not sufficiently wide enough to allow the incoming molecule to pass through it or certain constrictions in the tunnel block its delivery. This could be either to control the frequency of molecules traveling across or to coordinate and facilitate coupled reaction rates. Another possible scenario of transient tunnel formation is one in which the tunnel is nonexistent in the apo state, and only upon significant conformational change, under appropriate cues, is the tunnel formed. In several cases transient tunnels require intermediate/substrate-induced conformational changes in the tunnel residues to open up for the transport of the incoming molecule, within the respective enzyme. These tunnels undergo enormous fluctuations and switch between open and close states. It is remarkable that the presence of these conduits, which are as long as 20−30 Å and even longer like 96 Å in CPS,6a run inside the protein body, forming pores that serve as highways for transport of these gaseous molecules. In several cases, an added level of tuning into the tunnel architecture is introduced by incorporating gating mechanisms into the EG and IG tunnel architectures.

Gates serve as checkpoints and vary from system to system; some are as simple as an amino acid blocking the path which moves out upon receiving appropriate cues such as the swinging door type in cytidine triphosphate synthase (CTP) and in others more complex arrangement of amino acids come together to form control units such as aperture gates, drawbridge, and shell type gates. These tunnels and their gates are connected via an active communication network that spans between distal centers and hence introduces both conformation and dynamic allostery into the protein systems. It is not uncommon to observe long-distance allosteric networks that can be dynamic in nature and transiently formed via the motion of loop elements, secondary structural rearrangements, or of entire domains.

EXTERNAL GASEOUS (EG) TUNNEL ARCHITECTURES 
EG tunnels connect the bulk solvent with the active site of an enzyme. These tunnels are found in several enzymes that accept gaseous substrates to facilitate their delivery to the buried active site. A class of predominant gaseous substrates are alkanes such as methane and ethane gases that are oxidized aerobically or via anaerobic pathways. Recently,   the crystal structure of the enzyme that anaerobically oxidizes ethane to ethylCoM from Candidatus Ethanoperedens thermophilum was determined, and named it ethylCoM reductase. The enzyme belongs to the broad methylCoM reductase superfamily, which oxidizes methane. The ethylCoM reductase has a 33 Å tunnel that runs across the length of the protein. Interestingly, the EG tunnel present in ethylCoM reductase has some very unique features. At the end of the tunnel, near the Ni-cofactor F430 active site, there are several residues that are post-translationally modified. Methylated amino acids, such as S-methylcysteine, 3-methylisoleucine, 2(S)-methylglutamine, and N2 -methylhistidine line the tunnel. It is likely that these residues tune the enzyme to select for ethane by creating a very hydrophobic environment and prevent similar-sized hydrophilic molecules such as methanol from reaching the active center. The larger hydrophobic alkanes are selected out via optimization of the tunnel diameter, which is fit to accommodate ethane. Another example of an alkane transporting tunnel exists in soluble methane monooxygenase (sMMO) that performs C− H functionalization by breaking the strongest C−H bond, among saturated hydrocarbons, in methane and aerobically oxidizes it to form methanol. In methanotrophs, these enzymes are tightly regulated, and the complex formation between the two proteins, hydroxylase MMOH and regulatory protein MMOB, is required for function. The EG tunnel formed in this system is very hydrophobic, and the diameter is such that it only allows for smaller gases such as methane and O2 to percolate into the di-Fe cluster harboring active site. In Methylosinus trichosporium OB3b, half of the tunnel is at the interface of the MMOH/MMOB complex, and another half of the tunnel is buried within MMOH, where the oxidation reaction is catalyzed. As an added control feature, the complex has multiple gates to regulate its function. Residues W308 and P215 guard the entrance of the substrate molecules and block the formation of the EG tunnel in the absence of the complex between MMOH and MMOB.

Comment: This demonstrates and exemplifies how in many cases, single monomers have important functions, and changing them through mutations can remove the function of the entirety of the enzyme.  

Upon complexation, a conformational change is triggered, and these residues move out of the path, opening the passage for the entire tunnel. When the upper gating residues move upon MMOB/MMOH complex formation, another residue F282 right near the active site also concomitantly undergoes a shift, allowing methane and oxygen to access the di-Fe center. MMOH also has an alternative secondary hydrophilic passage, accessible only when MMOB/MMOH complex dissociates which allows the polar methanol product to be released through it. The gating residues, F282 in the hydrophobic EG tunnel and E240 in the hydrophilic passage, switch between open and close states alternately upon binding/unbinding of MMOB and hence opens one of the two tunnels at a time. This regulates the flow of substrates and products and avoids overoxidation of methanol by releasing it through the hydrophilic passage prior to the entry of substrates in the active site via the hydrophobic EG tunnel.

One of the most common gaseous substrates for which several examples of tunneling enzymes exist is oxygen (O2). It is used in several important oxidation reactions for the generation of essential pathway intermediates and also is a key transport gas in cells. Interestingly in several cases, oxygen is transported to the desired site via molecular tunnels, perhaps to modulate its flow. There are two types of tunnel architectures that are prevalent: first, where there is a main tunnel connected to several subsidiary tunnels, and second, those with fewer tunnels but with stringent gating controls. For instance, soybean lipoxygenase-1 is an example of a multitunnel system that has eight EG tunnels, out of which the one that is formed by hydrophobic residues, such as L496, I553, I547, and V564, has the highest throughput and is identified as the main gaseous tunnel for delivering O2 to the reaction center. It catalyzes the stereospecific peroxidation of linoleic acid via forming a pentadienyl radical intermediate. Under oxygen-deficient conditions, the intermediate escapes from the active site to the bulk and forms four products, i.e., 13S-, 13R-, 9S-, and 9R-hydroperoxy-octadecadienoic acid, in equal distributions. However, under ambient O2 conditions, the EG tunnel delivers O2 efficiently into the active site which has a properly positioned and oriented radical intermediate. Here, O2 is delivered by the EG tunnel such that it stereo- and regiospecifically attacks the radical intermediate to yield 13S-hydroperoxy-octadecadienoic acid as a major product with ∼90% yield. It has also been shown that when the EG tunnel residue L496 is mutated to a bulky tryptophan, it opens up a new gaseous tunnel for O2 delivery, where it attacks at the different side of the pentadienyl intermediate, preferring the formation of 9S- and 9Rproducts. This example showed the importance of the gaseous tunnel in determining the stereo- and regiospecificity for product formation

INTERNAL GASEOUS (IG) TUNNEL ARCHITECTURES 

While the EG tunnels transport gases and have pores that are accessible to the surface, there is another class of tunnels formed within the core of the enzyme system, buried in the body of the protein, called the IG tunnels. 

Question: How could these tunnels be the product of evolutionary pressures, requiring long periods of time, if, in case the tunnel that protects the toxic intermediates is not instantiated from the beginning, the products would leak, and eventually kill the cell? This is an all-or-nothing business, where these tunnels had to be created right from the start, fully set up and developed. 

These systems generally have the tunnel connecting two reactive centers, and the product of one reaction is transported to the second active site. In some cases, an IG tunnel network, instead of leading to another active site, can also lead to the lipid membrane so as to directly access the active site of membrane-bound enzymes. The substrate is generated within one of the active centers and is in the limiting amount as well as it could be toxic or unstable in the presented environment. Therefore, to ensure it reaches the destination reaction center, nature has devised strategies by constructing IG tunnels which, in several instances, are transient tunnels that only form upon entry of substates and have much more controlled and complex gating architectures. 57

Comment: This is truly fascinating evidence of intended design for important functions: To direct gases to where they are needed to perform a reaction.

Image description: The structure of carbamoyl phosphate synthetase 
The small subunit that contains the active site for the hydrolysis of glutamine is shown in green. The N-terminal domain of the large subunit that contains the active site for the synthesis of carboxy phosphate and carbamate is shown in red. The C-terminal domain of the large subunit that contains the active site for the synthesis of carbamoyl phosphate is shown in blue. The two molecular tunnels for the translocation of ammonia and carbamate are shown in yellow dotted lines 56

Nucleotide metabolism: By evolution? 

G. Caetano-Anollés (2013): The origin of metabolism has been linked to abiotic chemistries that existed in our planet at the beginning of life. While plausible chemical pathways have been proposed, including the synthesis of nucleobases, ribose and ribonucleotides, the cooption of these reactions by modern enzymes remains shrouded in mystery. Pathways of nucleotide biosynthesis, catabolism, and salvage originated ∼300 million years later by concerted enzymatic recruitments and gradual replacement of abiotic chemistries. The simultaneous appearance of purine biosynthesis and the ribosome probably fulfilled the expanding matter-energy and processing needs of genomic information. 59

Comment: These are assertions, clearly not based on scientific data and observations, but ad-hoc conclusions that lack evidence. 

I think that in recent years, atheists are more and more becoming aware that they are losing the battle in regard to teleological arguments. The force of the evidence is too strong to be rationally denied. That is especially true in regard to the origin and fine-tuning of the universe, the origin of the laws of physics, the origin of complex instructional information, and the irreducibility of biological systems.

One of the adopted tactics by those that have decided, that God cannot be permitted to give even the tiniest step into the door, is shifting from strong to weak atheism, in order to remove the burden of proof from their shoulders.

Another tactic in order not to look silly has been to avoid discussing design altogether, arguing about moral issues, and accusing the God of the Bible of being immoral, as Dawkins did famously in his book: The God delusion.

One of the questions raised and argued about recently, that I have seen, is: God is evil because he created evil. Since he had the foresight and knew that in this world, Adam and Eve would sin, and sin would enter the world, and since he did not prevent it, he is ultimately responsible for evil, therefore he is evil.

But is that so? What are the answers? Is God like a surgeon that permitted pain to achieve a greater good? Did he permit evil to display what goodness is, contrasting it with evil? Did he permit it in order to display his redemptive power, and put in practice his plan of salvation, demonstrating his love, and willingness to be graceful and merciful?

But was that justified, considering, as Jesus said and foresaw, that most would walk on the highway to hell? Is, putting everything on balance, the amount of suffering not greater than the amount of joy and happiness, only enjoyed by those saved?

My standard answer to this is: How could or should I have the capacity, based on my limited knowledge and perspective, to judge God's plan, and intentions, on a holistic scale?

Hell does not exist, because God is evil, but because he is just. Likewise, people do not go to hell because God is evil, but because man is sinful, and deserves to be punished for his evil deeds. A righteous God cannot let sin and evil remain unpunished, otherwise, he would have created an unjust world.

The made-up invented God in Islam is unjust. He forgives sins without punishment. Imagine: There is a rich man, that had his entire family kidnapped for a ransom. The rich man paid with all his belongings, but the kidnappers tortured and killed his entire family. Then they are cached and brought to the judge. The judge asks the (now) poor man: What shall I do with the perpetrators that annihilated your family, and ruined your life?

He says: Punish them accordingly, with the hardest punishment permitted by law. The criminals however say to the judge: Sir, please forgive us, be merciful, we are repenting for what we did. We are so sorry. Then the judge says: Ok, I attend to your demand. You can go.

How would the victim feel? Obviously, outraged and even worse than before. A price has to be paid in order for justice to be maintained. The principle: evil demands punishment is the foundation of justice and is untradeable. A holy and just God cannot let pass evil unpunished. It does not matter, if just a "harmless" lie, or perpetuating an unjust war for the sake of one's own greatness, glory, and power, at the cost of millions of deaths. Sin is sin, and demands punishment. A holy God cannot let sin go, unpunished. That is the principle applied in the Bible, by the God of the Bible. That's what distinguishes Jahweh from Allah. The two cannot be conciliated. One is a different God than the other. Claiming that the God of Islam is the same deity as the God of the Bible is silly.

Unbelievers complain that this world is unjust, and not the best possible world. On what ground?

Maybe you have heard the claim that the more science advances, the less God can hide in a gap of knowledge. Thats hogwash. The contrary is the case. The more science advances, the less naturalism can hide in the gaps of knowledge. See the state of knowledge a hundred years ago, and compare it to now:
Static eternal universe ---> Expanding finite-age universe
Ignorance of fine-tuning ---> knowledge of extensive fine-tuning
Cells are simple protoplasm, and to get life is a pretty simple pathway ---> naturalistic OOL is next-to-if, not impossible-to-explain
Biological systems are probably complicated ---> biological evolution of information-based and directed machines are next-to, if not -impossible-to-explain by unguided natural means.
The truth is, the more science advances, the more it points to an intelligent mind being the best explanation for all phenomena.
Unguided random events are implausible to the extreme.

"Cellular Communication: The amazing size of Information Exchange in the Human Body"

We have 37 trillion cells in our human body that communicate with each other, like a huge WWW.

The Human Genetic code information content is about 6 billion bits. The Epigenetic code information content is about ten times larger:≈ 60 billion bits, Sum, total, 66 billion bits.
To find the total estimated information content of the 37 trillion cells in the human body, we can multiply the 66 billion bits by the number of cells:

Total estimated information content = 66 billion bits × 37 trillion cells = 2.44 quintillion bits.

Now, let's compare this to the daily global internet traffic: Daily internet traffic ≈ 8 quintillion bits (8 x 10^18 bits)

Comparing the two values:

Total information content of human cells ≈ 2.44 quintillion bits (2.44 x 10^18 bits)
Daily internet traffic ≈ 8 quintillion bits (8 x 10^18 bits)

The daily global internet traffic (8 quintillion bits) is roughly three times larger than the estimated total information content within the 37 trillion cells in the human body (2.44 quintillion bits).
So the information content in the cells of 3 people is equal to all information exchange on the worldwide web, per day !!

Each cell contains about 2,3 billion proteins, and molecular machines. 20 thousand genes, which can be expressed in different ways, giving rise to 6 million protein species, through the spliceosome, which can splice the same gene over 300 times, giving rise to different gene products. The information can be read forward, or backward, with different reading frames. Life, in special complex life, is permeated with communication systems, that are employed  

Each cell contains over 100 different epigenetic languages and codes, that work in an interdependent fashion together. These languages crosstalk with each other, dozens of them. Furthermore:  

Wide-ranging conversations among various organelles respond to cell stress and provide quality control for mitochondria, membranes, and the production of proteins. Elaborate signaling inside neurons provides precise transport of materials along the axon and allows complex decision-making to take place among multiple compartments in dendrites.

We are also learning about how the primary cilium might function as a cell’s central control center, as sort of the “brain” of a cell, with its tubular structure used as an antenna for signaling.  Long considered independent, the microtubule and actin network systems are now known to engage in functional cross-talk to drive essential cellular processes such as whole-cell migration, mitotic spindle positioning, or cell-wide organelle transport.

Cell-Cell interactions are performed in multicellular organisms through a sophisticated intercellular communication machinery. There are many ways like gap junctions and exosomes. But recently, it has been discovered that Cells talk and help each other via tiny tube networks. Cells are known to use intracellular microtubules, veritable nanotubular highways which direct proteins to their correct final destination inside of Cells. But, remarkably they are also used for intercellular communication, from Cells to Cells, and furthermore, for organelle Transport between Cells.

Just as humans use letters and words to create messages, cells release molecules called ligands into the environment to send messages to their neighbors—such as an instruction to differentiate or proliferate. The ligands bind to receptors on the surface of other cells, which interpret the message and trigger a set of chemical reactions to relay it to the correct molecules in the cell's interior.

One major communication channel is called the bone morphogenetic protein (BMP) pathway, which operates in nearly all tissues. This system uses many different ligands and receptors in various combinations.

1,894 ligand-receptor pairs—based on 642 ligands and 589 receptors— have been reported in the literature so far, and drew up a large-scale map of cell-to-cell. Most cells express tens or even hundreds of ligands and receptors, creating a highly connected signaling network made up of cell types that can communicate with each other through multiple ligand-receptor paths.

When biting into an apple, the body will immediately signal a complex sequence of messages and processes to break down the apple into energy and essential structural nutrients for cellular repair and replacement. That initial signal activates communication throughout the entire body, enabling metabolism to send support to every facet of the organisms function, be it mental, emotional or physical. Health and performance are completely dependent upon how efficient that signalling and communication process works.

Cells and tissues work together and respond to changes in the internal and external environment.  Epigenetic mechanisms refer to heritable changes in gene expression that occur without changes in the DNA sequence. These mechanisms involve modifications to the structure of DNA and histone proteins that affect how genes are activated or silenced. Epigenetic languages enable cells to differentiate into various specialized cell types during development and play a vital role in maintaining cell identity and function throughout an organism's life. Epigenetic languages help determine which genes are active or inactive in specific cells, influencing processes such as cell growth, differentiation, and response to environmental cues.

Communication theory, specifies five stages for any communication system, regardless of its form: an information source, an encoder, a communication channel, a decoder (or receiver), and a user. The information source generates the information to be transmitted; the encoder transforms the information into a suitable message form for transmission over the communication channel; and the decoder performs the inverse operation of the encoder, or approximately so, for the user at the other end of the channel.

1. A living cell is an information-driven factory. The human body is like a huge city of interlinked factories, that work in a joint venture, together.
2. The information drives the operation in a manner analogous to how software in a computer drives computer hardware.
3. Computers are the product of deliberate intelligent action, not random processes.

Unveiling the convergence, how science points to creation

In scientific discovery, moments of profound revelation have punctuated our understanding of the cosmos and life's origins. The journey began with the proclamation of the Big Bang theory in 1931, conceived by Georges Lemaître. This monumental theory unveiled the birth of the universe itself, a cataclysmic event that set the stage for everything that followed. Then, in a parallel avenue of inquiry, 2007 brought forth another groundbreaking notion—the Biological Big Bang model. Eugene Koonin's audacious proposal illuminated the grand transitions in biology, suggesting that life's progression, much like the universe's, was marked by sudden transformative leaps. In 2013, the words of Wilhelm Huck, a chemist from the Netherlands, said that a functioning cell must possess intricate correctness from the very outset, corroborating the concept of irreducible complexity and interdependence underscoring the astonishing complexity of life's origin and development and that life had to emerge all at once, in all its complexity, and not in a gradualistic fashion, like proposed by chemical evolution. 

And now, in 2023, the James Webb Space Telescope delivers a revelation that amplifies this theme of swift emergence. Its gaze deep into the past has uncovered the Universe's early beginning, a crescendo of star formation bursts. The NASA article published on June 5th succinctly captures this newfound insight into the cosmos. It's a revelation that harmonizes with the overarching narrative—one of sudden emergence and creation. NASAs article from Jun 5, 2023 states: Early Universe Crackled With Bursts of Star Formation, Webb Shows

Remarkably, this pace of discovery harmonizes with an ancient account—a narrative of creation that transcends centuries. The echo of Genesis resonates anew as the scientific narrative and the scriptural testimony align. Science, with its probing inquiry, and the words of the Bible, rooted in faith, converge on a shared revelation. The culmination of knowledge and spiritual understanding bears witness to the profundity of our era. Imagine the awe that would have stirred in the hearts of our forebears, those devout believers who anchored their faith in God's design. They would have marveled at the unveiled truths manifesting before our eyes today. In the tableau of unfolding knowledge, God's word stands unswervingly faithful and true, its wisdom echoing through the ages.

Indeed, we stand on the cusp of an extraordinary epoch—a moment when the threads of discovery weave together intricate patterns of understanding. The convergence of science and faith, of empirical exploration and sacred revelation, paints a portrait of a universe and life that burst forth suddenly, in resplendent complexity. As witnesses to this convergence, we are privileged to see the harmony between the cosmic genesis and the divine Creator—an affirmation that resounds with resolute clarity in the tapestry of our existence.

In conclusion, first, science had the first surprise, with the Big Bang of the Universe, first proposed by Lemaitre in 1931. Then, in 2007, Eugene Koonin, proposed:  The Biological Big Bang model for the major transitions biology.  In 2013, Wilhelm Huck,  Chemist stated:  A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity. And now, in 2023, the JWebb telescope makes another startling revelation: Early Universe Crackled With Bursts of Star Formation, Webb Shows, the title of a NASA news article, published on the 5th of June, states. Science and the Bible converge to the same outcome, and science confirms the Bible.

Examining 47 crucial processes that influence the development, structure, and function of organisms reveals some astonishing interconnections

The sheer complexity and intricate interdependence observed in biological systems provide a strong foundation for arguments in favor of Intelligent Design (ID).  Developmental biology encompasses a wide range of processes that dictate the growth, form, and function of organisms from conception to maturity. The following list encompasses processes ranging from the molecular to the organ level, each vital for the proper development, structure, and function of an organism. These processes, often interlinked, collectively orchestrate the intricate dance of development from a single cell to a multicellular organism.

1. Angiogenesis and Vasculogenesis: Formation of new blood vessels from pre-existing ones (angiogenesis) and de novo vessel formation (vasculogenesis).
2. Apoptosis: Programmed cell death essential for removing unwanted cells.
3. Cell-Cycle Regulation: Controls the progression of cells through the stages of growth and division.
4. Cell-cell adhesion and the ECM: Refers to how cells stick to each other and to the extracellular matrix, essential for tissue formation.
5. Cell-Cell Communication: Cells communicate to coordinate their actions.
6. Cell Fate Determination and Lineage Specification (Cell differentiation): Process by which cells become specialized in their function.
7. Cell Migration and Chemotaxis: Movement of cells, guided by certain chemical gradients.
8. Cell Polarity and Asymmetry: Defines distinct cellular 'sides' or 'ends', crucial for many cell functions.
9. Cellular Pluripotency: Cells can give rise to multiple cell types.
10. Cellular Senescence: State of stable cell cycle arrest.
11. Centrosomes: Organize microtubules and provide structure to cells.
12. Chromatin Dynamics: How DNA and proteins are organized in the nucleus.
13. Cytokinesis: Physical process of cell division.
14. Cytoskeletal Arrays: Framework of the cell, involved in cell shape, movement, and division.
15. DNA Methylation: Addition of methyl groups to DNA, often involved in gene silencing.
16. Egg-Polarity Genes: Determine the axes of the egg and subsequently the organism.
17. Epigenetic Codes: Changes in gene function without changing DNA sequence.
18. Gene Regulation Network: Interactions between genes, controlling when and where genes are expressed.
19. Germ Cell Formation and Migration: Development and movement of reproductive cells.
20. Germ Layer Formation (Gastrulation): Development of primary tissue layers in embryos.
21. Histone PTMs: Modifications to histone proteins affecting DNA accessibility.
22. Homeobox and Hox Genes: Control the body plan of an embryo along the head-tail axis.
23. Hormones: Chemical messengers coordinating bodily functions.
24. Immune System Development: Formation and maturation of immune cells.
25. Ion Channels and Electromagnetic Fields: Channels allowing ions to flow in/out of cells; electromagnetic fields can influence development.
26. Membrane Targets: Processes focusing on cell membrane components.
27. MicroRNA Regulation: Small RNAs regulating gene expression post-transcriptionally.
28. Morphogen Gradients: Concentration gradients of substances determining tissue development.
29. Neural Crest Cells Migration: Movement of cells contributing to diverse structures, including peripheral nerves.
30. Neural plate folding and convergence: Formation of the neural tube in early development.
31. Neuronal Pruning and Synaptogenesis: Refinement of neural connections and formation of synapses.
32. Neurulation and Neural Tube Formation: Development of the neural tube, precursor to the CNS.
33. Noncoding RNA from Junk DNA: RNA molecules not coding for protein but having various functions.
34. Oogenesis: Egg cell (oocyte) formation.
35. Oocyte Maturation and Fertilization: Development of mature egg and its fusion with sperm.
36. Pattern Formation: Processes determining organized spatial arrangement of cells/tissues.
37. Photoreceptor development: Formation of cells detecting light in the eye.
38. Regional specification: Defining distinct regions within developing tissues.
39. Segmentation and Somitogenesis: Division of body into segments and formation of somites in embryos.
40. Signaling Pathways: Series of molecular events relaying extracellular signals to intracellular targets.
41. Spatiotemporal gene expression: Time and place-specific gene expression.
42. Spermatogenesis: The process of sperm cell formation and maturation.
43. Stem Cell Regulation and Differentiation: Control of stem cell fate and their development into specialized cells.
44. Symbiotic Relationships and Microbiota Influence: Interactions with microbial partners and their influence on host development.
45. Syncytium formation: Multinucleated cell formation, especially important in muscle tissues.
46. Transposons and Retrotransposons: Mobile genetic elements, sometimes influencing gene regulation.
47. Tissue Induction and Organogenesis: Formation of tissues and organs from undifferentiated cells.

The processes and systems listed are essential to the complex orchestration of development and physiology in multicellular organisms. Many of these are interwoven and interdependent to ensure accurate and timely development, function, and maintenance. It's worth noting that this list only scratches the surface. The interconnectedness of these systems is immensely complex, with each one potentially influencing or being influenced by multiple others. They collectively underscore the intricacy and delicate choreography inherent to biology. 

1. Harmony in Complexity

The vast array of processes, ranging from the microscopic level (like DNA methylation) to the macroscopic (like organogenesis), are so tightly interwoven that a disturbance in one can drastically impact another. This finely-tuned orchestration suggests a system that has been designed with precision and purpose, rather than one that arose from a series of unplanned, random events.

Chromatin Dynamics and Epigenetic Codes

Chromatin Dynamics (Point 12): At the microscopic level, chromatin dynamics describes how DNA and proteins are organized within the nucleus. DNA wraps around histone proteins, forming nucleosomes. The compactness of this structure dictates whether genes are accessible for transcription or not. Changes in chromatin structure play an essential role in controlling which genes are active at any given time.
Epigenetic Codes (Point 17): Epigenetics encompasses changes in gene function that don't involve alterations to the underlying DNA sequence. One of the primary mechanisms for this is DNA methylation (Point 15), where methyl groups are added to the DNA, usually leading to gene silencing.

Interdependencies and Implications

Gene Regulation Network (Point 18): Chromatin dynamics and epigenetic modifications directly influence the gene regulatory networks. These modifications decide which genes are turned on or off, ensuring that cells have the appropriate responses to environmental cues.
Cell Fate Determination and Lineage Specification (Point 6): Epigenetic codes and chromatin remodeling play crucial roles in determining cell fate. For instance, a stem cell's decision to become a muscle cell versus a nerve cell can be influenced by these modifications.
Tissue Induction and Organogenesis (Point 47): Proper tissue and organ formation requires specific sets of genes to be activated in a timely and spatial manner. Chromatin dynamics and epigenetic modifications help coordinate these gene expression patterns, ensuring organs form correctly and functionally.

Given the interplay between chromatin dynamics and epigenetic codes, one can see the harmony in complexity. If chromatin isn't organized correctly, or if the epigenetic codes go awry, the ripple effects can be vast, impacting everything from individual cell functions to the development of entire organs. Such a tightly coordinated system, where microscopic modifications can influence macroscopic outcomes, speaks to a design with intricate precision and purpose.

2. A House of Cards

Many proponents of ID describe the cellular processes and systems as a "house of cards." In this analogy, removing one card (or disrupting a single process) may cause the entire structure to collapse. Such intricate dependencies make it hard to envision a gradual, step-by-step evolutionary development. How would the system function if even one of its myriad processes was not yet in place?

Let's take a look into Cell-Cell Communication and its relevance to many of the processes listed previously.

Cell-Cell Communication and the Notch Signaling Pathway

In multicellular organisms, cells don't function in isolation. They constantly communicate with one another to maintain harmony and respond to changes in the environment. One of the most studied pathways in this realm is the Notch signaling pathway.

How Notch Signaling Works

Activation: Notch signaling is initiated when a ligand from a neighboring cell binds to the Notch receptor of another cell.
Cleavage and Migration: This binding event causes two proteolytic cleavages of the Notch receptor. The second cleavage releases the Notch intracellular domain (NICD), which then migrates to the cell's nucleus.
Gene Expression: Once inside the nucleus, the NICD associates with other proteins and acts as a transcriptional activator, turning on genes that will affect the cell's fate.
Interdependencies and Systems Biology Implications:

Cell Differentiation (Point 6): Notch signaling plays a critical role in determining cell fate and ensuring cells differentiate into the types needed for proper tissue and organ function.
Pattern Formation (Point 36): The pathway helps establish patterns of cells in tissues, ensuring the right cells are in the right places.
Gene Regulation Network (Point 18): Notch signaling interfaces with numerous other pathways, making it a node in the complex web of cellular communication. Disruptions here can have cascading effects on numerous processes.
Tissue Induction and Organogenesis (Point 47): Proper tissue formation often requires communication between cells, with Notch signaling being pivotal for many of these interactions.

Considering the Notch signaling pathway alone, it's evident that its perturbation can disrupt multiple processes. From a systems biology perspective, if this pathway wasn't functioning correctly or was only partially developed, it's challenging to see how many critical developmental processes would proceed effectively. Its intricate ties to various cellular and developmental processes underscore the vast interconnectedness in biological systems.

3. Irreducible Complexity

A cornerstone of the ID argument is that many biological systems are "irreducibly complex." This means that they need all their parts to be present and functioning simultaneously to work. In the vast web of interconnected processes, where one relies on another to operate, the absence or malfunctioning of even one process would render the whole system dysfunctional. This poses significant challenges to the idea of gradual evolution: if a system needs all its parts to function, how could it evolve piecemeal over time?

Epigenetic Regulation and Gene Expression

Taking a look at the list of 47 points, there is a profound interdependence between "DNA Methylation" (Point 15), "Epigenetic Codes" (Point 17), "Gene Regulation Network" (Point 18), and "MicroRNA Regulation" (Point 27).

DNA Methylation (Point 15): This involves the addition of a methyl group to a cytosine base in DNA. Methylation typically suppresses gene transcription, and thus, it's a mechanism by which genes can be "turned off."
Epigenetic Codes (Point 17): Epigenetics refers to changes in gene function without altering the DNA sequence itself. Methylation is an epigenetic modification, but there are others, such as histone modifications, which can impact how tightly DNA is wound around histone proteins, thereby regulating gene accessibility and expression.
Gene Regulation Network (Point 18): This is a complex network of interactions between genes, typically involving transcription factors, enhancers, silencers, and other regulatory elements that control when, where, and how genes are expressed.
MicroRNA Regulation (Point 27): MicroRNAs are small RNA molecules that do not code for proteins. Instead, they regulate gene expression post-transcriptionally. They can bind to messenger RNA (mRNA) molecules and prevent them from being translated into proteins, or even lead to their degradation.

The interdependedness between these processes ensures precise control over gene expression. For an organism to develop and function properly, genes need to be turned on and off at the right times and in the right places. But consider this: if DNA methylation patterns are awry, then certain genes might be wrongly activated or suppressed. The gene regulatory network relies on correct epigenetic codes to function properly, and aberrant microRNA expression can disrupt the entire balance.  These systems' mutual dependencies make it challenging to envision how they could have evolved separately or in a stepwise fashion. For example, if a regulatory gene network evolved before the epigenetic controls were in place, how would it ensure precision in gene expression? If microRNAs emerged but the system to process them or the targets they bind to weren't present, would they confer any advantage?
This web of interdependence between epigenetic modifications, gene networks, and microRNA regulation exemplifies the intricacies and precision of cellular processes, underscoring the challenges faced by piecemeal evolutionary explanations.

4. The Language of Life

The cell operates with a myriad of 'codes' and 'languages.' From the genetic code in DNA to the intricate signaling pathways and feedback loops, cells communicate and operate in a way that is reminiscent of an intricately coded software program. The emergence of such a detailed and error-proof 'language system' from random events appears statistically implausible and points towards a designed system.

Neural Blueprint and Information Transfer

To showcase the interdependence within the 47 points, let's focus on the intricate processes associated with neural development and communication. Consider the following components:

Neural plate folding and convergence (Point 30): Early in development, the neural plate undergoes specific movements and foldings to form the neural tube, the precursor of the central nervous system. This requires accurate spatial organization.
Neurulation and Neural Tube Formation (Point 32): Once the neural plate has folded, it must properly close to form the neural tube. This structure eventually gives rise to the brain and spinal cord.
Cell-Cell Communication (Point 5): Cells must communicate effectively to coordinate these early developmental processes. Miscommunication or errors in signaling can lead to severe developmental defects.
Gene Regulation Network (Point 18): A precise network of gene interactions ensures that the right genes are activated (or suppressed) at the right times for neural tube formation.
Morphogen Gradients (Point 28): These are concentration gradients of substances that dictate tissue development. In the context of neural development, morphogens play critical roles in specifying which parts of the neural tube become the brain and which become the spinal cord.
Homeobox and Hox Genes (Point 22): These genes play a pivotal role in setting up the body plan of an embryo along its head-tail axis, including defining regions of the developing brain and spinal cord.

From a system's biology perspective, neural development is a marvel of coordination and communication. For the neural tube to form correctly, cells must communicate with each other, adhere to each other in specific ways, respond to morphogen gradients, and activate the right genes at the right times. All these processes are tightly interwoven, and a failure in one process can impact others. For instance, if the gene regulatory network doesn't activate the right set of genes due to some perturbation, it could potentially affect the morphogen gradients, which in turn might disturb the proper folding of the neural plate, leading to defects in neural tube formation. Given the intricate dance between these processes, it's hard to fathom how such a system could have evolved piecemeal. Without the precise coordination of these multiple factors, the entire process of neural development could be jeopardized. This mutual dependency paints a picture of an orchestrated design where all parts must work in concert for the successful creation of such a complex system.

5. Feedback Loops and Regulatory Mechanisms

The numerous feedback loops and regulatory mechanisms ensure that every cellular process is meticulously monitored and adjusted as necessary. The foresight required for such intricate regulation seems beyond the scope of random mutations and natural selection.

Tissue Development and Maintenance

Diving into the intricate world of cellular growth, differentiation, and communication, let's explore the interwoven dance of several processes from the 47 points:

Cell-Cycle Regulation (Point 3): Cells have inbuilt systems that control their growth and division. A cell must decide when to divide, based on numerous external and internal cues.
Apoptosis (Point 2): Paradoxically, while some cells are growing and dividing, others are programmed to die, ensuring that tissues are sculpted properly and potential rogue cells are eliminated.
Signaling Pathways (Point 40): These pathways relay extracellular signals to intracellular targets, determining whether a cell divides, differentiates, or dies.
Cell Fate Determination and Lineage Specification (Point 6): Within a developing tissue or organ, cells are assigned specific roles. This involves a complex interplay of signals that tell cells to differentiate into one type of cell versus another.
Epigenetic Codes (Point 17): These are modifications to the DNA or associated proteins that don't change the DNA sequence but control gene activity. Epigenetic changes can be induced by environmental factors and can influence cellular decisions like differentiation.
MicroRNA Regulation (Point 27): Small RNAs that don't code for protein but regulate other genes post-transcriptionally. These can fine-tune cellular responses by adjusting the levels of specific proteins in a cell.
Feedback Loops and Hormones (Point 23): Chemical messengers, like hormones, often function within feedback loops, where the output of a system acts as an input to control its behavior, ensuring homeostasis.
Tissue Induction and Organogenesis (Point 47): The formation of specific tissues and organs requires a concert of the above processes. Cells need to grow, communicate, decide their fate, differentiate, or even undergo programmed death, all under the watchful eyes of regulatory networks.
Morphogen Gradients (Point 28): Concentrations of specific molecules in an embryo provide cues to cells, guiding them in their development and spatial organization within tissues and organs.

In this intricate interdependence of cellular processes, each is indispensable. For tissue development and organogenesis to occur correctly, cells need the right mix of growth signals, differentiation cues, and spatial information. If signaling pathways go awry, it can lead to unchecked growth or improper differentiation. If apoptosis doesn't function correctly, it might lead to malformations or predispose tissues to cancers. If epigenetic codes aren't set right, genes essential for proper function might remain silent or get inappropriately activated. All these processes interlock in an elegant dance, each reliant on the other, ensuring that tissues and organs develop properly. Given the sheer complexity and the tight interdependence of these systems, one can argue the challenges it poses to a purely stepwise evolutionary process.

6. Information Storage and Retrieval

The cell's ability to store, retrieve, and implement vast amounts of information is unmatched. DNA, often likened to a data storage system, holds the blueprints for the entire organism. The intricate processes by which this information is accessed, read, and executed seem to be beyond the capacity of unguided evolutionary processes to produce.

Orchestrating Organism Development

Consider the awe-inspiring journey of a single fertilized egg (zygote) as it develops into a complex multicellular organism:

Oogenesis (Point 34) & Spermatogenesis (Point 42): The journey of life begins with the formation of gametes. These processes create the mature egg and sperm, each responsible for carrying half of the genetic information that will lead to a new organism. This initial formation of gametes is foundational to the progression of life.
Oocyte Maturation and Fertilization (Point 35): Following the formation of these gametes, the next step in the dance of life is their fusion. Once the oocyte and sperm unite, a zygote emerges, endowed with a complete set of DNA. This DNA is the architectural blueprint that directs the growth and development of the entire organism.
Gene Regulation Network (Point 18): As the zygote's journey begins, a need for orchestration arises. The gene regulation network offers this orchestration, a vast interconnected web of interactions, determining when, where, and how genes get expressed. This system can be visualized as a master conductor, deciding which sections of the orchestra play and at which moments.
Epigenetic Codes (Point 17): Complementing the conductor, there are specific markers, akin to bookmarks on our DNA, that dictate which musical notes (genes) are emphasized and which are muted. Epigenetic modifications ensure that certain genes are made accessible while others remain silent, all without altering the original score (DNA sequence).
MicroRNA Regulation (Point 27) & Noncoding RNA from Junk DNA (Point 33): Just as a symphony may require fine-tuning, these molecules offer a layer of adjustment to the genetic output after the primary transcript, enhancing or modulating the performance as necessary.
Cell-Cycle Regulation (Point 3): With the foundational notes set, the zygote embarks on a growth journey. This growth is meticulously orchestrated, ensuring that each cellular division is harmonious, with DNA replicated with precision.
Germ Layer Formation (Point 20): As this cellular symphony continues, differentiation begins, setting the stage for the future tissues and organs. Cells start aligning into three primary sections or layers: ectoderm, mesoderm, and endoderm, each layer contributing unique notes to the life song.
Cell Fate Determination and Lineage Specification (Point 6): Within these layers, the individual notes (cells) are further refined and specialized, ensuring that each plays its part in the evolving melody of life.
Signaling Pathways (Point 40) & Morphogen Gradients (Point 28): Communication becomes pivotal as cells continue to evolve and find their position in the overarching composition. These pathways and gradients act as messengers, ensuring each cell understands its role and positioning.
Tissue Induction and Organogenesis (Point 47): The crescendo approaches as cells, driven by unique cues, assemble to form the organs that are vital to life, such as the heart, lungs, and liver.
Cell-Cell Communication (Point 5) & Cell-cell adhesion and the ECM (Point 4): And as the composition reaches its zenith, for the entire system to function harmoniously, cells must communicate and connect, ensuring that every note is in place, creating a beautifully coordinated melody of life.

The life of an organism, as illustrated, is a complex interplay of various systems and processes, each building upon the other, forming a harmonious melody from inception to maturity. This journey, from a single cell to a fully formed organism, involves accessing, reading, and executing a vast amount of information stored within the DNA. At each step, multiple processes from the 47 points are at play, acting like meticulous architects interpreting and building a structure based on an intricate blueprint. Given the precision, coordination, and depth of information involved, it offers a profound reflection on the cell's unmatched information storage and retrieval system.

The intricate interdependence and sheer complexity observed in biological systems make it hard to reconcile with a purely evolutionary framework that relies on random mutations and natural selection. The precision, foresight, and harmony seen in these systems appear to be indicative of a design by an intelligent agent.

Interdependence and Intricacy in Biological Systems

When one looks at the formation and development of complex multicellular organisms, it's akin to witnessing a grand orchestra, where each musician (or process) plays an essential part in crafting a collective, harmonious sound. If even one musician is missing or plays out of tune, the entire performance can be compromised. Similarly, the 47 biological processes are so deeply interwoven that a disturbance or absence in even a single process can lead to systemic disruptions. 

Foundational Importance: Just as an orchestra requires foundational instruments like percussion to set the rhythm, processes such as Oogenesis, Spermatogenesis, and Oocyte Maturation and Fertilization set the stage for life's beginning. Without these processes, the journey wouldn't even commence.
Regulation and Coordination: Once the foundational processes are in place, the need for regulation and coordination becomes paramount. The Gene Regulation Network, MicroRNA Regulation, and Epigenetic Codes serve as the conductors and coordinators, ensuring each 'musician' performs at the right time and in harmony with others.
Specialization and Differentiation: As the performance unfolds, specialized instruments like woodwinds or strings introduce unique melodies. Similarly, the Germ Layer Formation and Cell Fate Determination ensure cells differentiate and specialize, adding complexity to the organism's developmental 'symphony'.
Communication: In any orchestra, musicians must listen to and be in sync with each other. The biological equivalents are the Signaling Pathways and Cell-Cell Communication, which guarantee that cells 'listen' to each other and respond appropriately, maintaining the organism's intricate harmony.
Structural Integrity: Just as each section of an orchestra relies on the structure and positioning of its musicians, processes like Cell-cell adhesion and the ECM ensure the physical structure and integrity of tissues and organs.
Systemic Harmony: Finally, all these processes need to work in tandem. Tissue Induction, Organogenesis, and other processes ensure the organism's 'performance' is harmonized from start to finish.

Implications for Evolution and Complexity

The interconnectedness and dependency of these processes pose intriguing questions about the evolution of complex life. The traditional evolutionary model suggests a gradual accumulation of beneficial mutations over time. However, when considering irreducible complexity, a challenge arises: How can systems that rely so heavily on the simultaneous functioning of multiple components evolve incrementally? Such systems seem to defy a piecemeal evolutionary development, as the system wouldn't function (or would offer no evolutionary advantage) until all components are present and working together. The development of multicellular organisms is a marvel of complexity, coordination, and precision, revealing the awe-inspiring intricacies of life.

The Fine Balance of Life

Redundancy and Flexibility: While it's true that the intricacies of these systems point towards an irreducible complexity, nature has also ingeniously incorporated redundancy and flexibility. There are instances where multiple processes can achieve a similar outcome or where systems have backup mechanisms. This 'buffer' allows organisms to survive and adapt in fluctuating environments and under various stresses.
Fine-tuning: These systems are optimized for efficiency and effectiveness. Each process, while essential, has likely been the subject of countless iterations, shaped by environmental pressures and interactions with other processes. This ongoing 'tuning' has resulted in the beautifully orchestrated dance of cellular and molecular events we observe today.
The Starting Point of Complexity:  If even the most primitive unicellular organisms required a subset of these 47 processes to survive, then how could such complexity arise spontaneously without guidance? The leap from non-life to even the simplest life form is monumental, given the intricate machinery required at the cellular level. Such complexity, right from the beginning, suggests a purposefully designed set up. 
The Problem of Incremental Evolution:  How can a partial system, that's non-functional until fully formed, provide a selective advantage? Without the advantage, the process won't be 'selected' and thus, won't evolve. If the machinery of the cell works like a finely tuned watch, missing one gear might render it non-functional. Evolutionary processes can't favor non-functional or less functional states.
The Interconnectedness Challenge: The interconnected nature of the 47 processes outlined implies that changes in one system could have ripple effects across others. A random mutation in one part might require synchronized changes in several others to maintain functionality. Such a level of concurrent and harmonized change seems beyond the capabilities of random mutation and natural selection.
Plasticity and Pre-programming: The capacity for organisms to adapt to their environment is often touted as evidence for evolution. However,  this plasticity is evidence of pre-programmed adaptability—a foresight that allows organisms to respond to changing environments. Rather than being proof of random evolution, this built-in adaptability may suggest a designer who anticipated the varied and dynamic environments the organism would encounter.
Information Theory: One significant point is the infusion of information into the DNA. Information, as we understand it in other realms (like coding or linguistics), typically arises from intelligence. The intricate and specific information carried in the DNA, guiding the myriad of processes in the organism, is clear evidence of an intelligent input.[/size]

Eukaryotes

As everywhere through evolutionary biology, the claim is that things went from less, to more complex, over long periods of time. 

D. A. Peattie:  The eukaryote has structural features that allow it to communicate better than prokaryotes, features that permit cellular aggregation and multicellular life. In contrast, the more primitive prokaryotes are less well-equipped for intercellular communication and cannot readily organize into multicellular organisms. Not only do eukaryotic cells allow larger and more complex organisms to be made, but they are themselves larger and more complex than prokaryotic cells. Whether eukaryotic cells live singly or as part of a multicellular organism, their activities can be much more complex and diversified than those of their prokaryotic counterparts. In prokaryotes, all internal cellular events take place within a single compartment, the cytoplasm. Eukaryotes contain many subcellular compartments, called organelles. Even single-celled eukaryotes can display remarkable complexity of function; some have features as specialized and diverse as sensory bristles, mouth parts, muscle-like contractile bundles, or stinging darts.


Structure of a typical animal cell

On a very fundamental level, eukaryotes and prokaryotes are similar. They share many aspects of their basic chemistry, physiology and metabolism. Both cell types are constructed of and use similar kinds of molecules and macromolecules to accomplish their cellular work. In both, for example, membranes are constructed mainly of fatty substances called lipids, and molecules that perform the cell's biological and mechanical work are called proteins.
Eukaryotes and prokaryotes both use the same chemical relay system to make protein. A permanent record of the code for all of the proteins the cell will require is stored in the form of DNA. Because DNA is the master copy of the cell's (or organism's) genetic make-up, the information it contains is absolutely crucial to the maintenance and perpetuation of the cell. As if to safeguard this archive, the cell does not use the DNA directly in protein synthesis but instead copies the information onto a temporary template of RNA, a chemical relative of DNA. Both the DNA and the RNA constitute a "recipe" for the cell's proteins. The recipe specifies the order in which amino acids, the chemical subunits of proteins, should be strung together to make the functional protein. Protein synthesis both in eukaryotes and prokaryotes takes place on structures called ribosomes, which are composed of RNA and protein. This illustrates one way in which prokaryotes and eukaryotes are similar and highlights the idea that differences between these organisms are often architectural. In other words, both cell types use the same bricks and mortar, but the structures they build with these materials vary dramatically.

The prokaryotic cell can be compared to a studio apartment: a one-room living space that has a kitchen area abutting the living room, which converts into a bedroom at night. All necessary items fit into their own locations in one room. There is an everyday; washable rug. Room temperature is comfortable-not too hot, not too cold. Conditions are adequate for everything that must occur in the apartment, but not optimal for any specific activity. In a similar way, all of the prokaryote's functions fit into a single compartment. The DNA is attached to the cell's membrane. Ribosomes float freely in the single compartment. Cellular respiration-the process by which nutrients are metabolized to release energy-is carried out at the cell membrane; there is no dedicated compartment for respiration. A eukaryotic cell can be compared to a mansion, where specific rooms are designed for particular activities. The mansion is more diverse in the activities it supports than the studio apartment. It can accommodate overnight guests comfortably and support social activities for adults in the living room or dining room, for children in the playroom. The baby's room is warm and furnished with bright colors and a soft, thick carpet. The kitchen has a stove, a refrigerator and a tile floor. Items are kept in the room that is most appropriate for them, under conditions ideal for the activities in that specific room. A eukaryotic cell resembles a mansion in that it is subdivided into many compartments. Each compartment is furnished with items and conditions suitable for a specific function, yet the compartments work together to allow the cell to maintain itself, to replicate and to perform more specialized activities.

Taking a closer look, we find three main structural aspects that differentiate prokaryotes from eukaryotes. The definitive difference is the presence of a true (eu) nucleus (karyon) in the eukaryotic cell. The nucleus, a double-membrane casing, sequesters the DNA in its own compartment and keeps it separate from the rest of the cell. In contrast, no such housing is provided for the DNA of a prokaryote. Instead the genetic material is tethered to the cell membrane and is otherwise allowed to float freely in the cell's interior. It is interesting to note that the DNA of eukaryotes is attached to the nuclear membrane, in a manner reminiscent of the attachment of prokaryotic DNA to the cell's outer membrane. 28

The greatest discontinuity in evolution: The gap from prokaryotes to eukaryotes



Ro Y. STANIER et. al., (1963) “The basic divergence in cellular structure, which separates the bacteria and blue-green algae from all other cellular organisms, represents the greatest single evolutionary discontinuity to be found in the presentday world” 31

E. V. Koonin (2002):The eukaryotic chromatin remodeling machinery, the cell cycle regulation systems, the nuclear envelope, the cytoskeleton, and the programmed cell death (PCD, or apoptosis) apparatus all are such major eukaryotic innovations, which do not appear to have direct prokaryotic predecessors.25

E. Derelle et.al.,(2006): The unicellular green marine alga Ostreococcus tauri is the world's smallest free-living eukaryote known to date, and encodes the fewest number of genes. It has been hypothesized, based on its small cellular and genome sizes, that it may reveal the “bare limits” of life as a free-living photosynthetic eukaryote, presumably having disposed of redundancies and presenting a simple organization and very little noncoding sequence. 27 It has a genome size of 12.560,000 base pairs, 8,166 genes and 7745 proteins. in comparison, the simplest free-living bacteria today is Pelagibacter ubique get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.

T. Cavalier-Smith (2010):  This radical transformation of cell structure (eukaryogenesis) is the most complex and extensive case of quantum evolution in the history of life. Beforehand earth was a sexless, purely bacterial and viral world. Afterwards sexy, endoskeletal eukaryotes evolved morphological complexity: diatoms, butterflies, corals, whales, kelps, and trees 32

E. Szathmáry (2015): The divide between prokaryotes and eukaryotes is the biggest known evolutionary discontinuity. There is no space here to enter the whole maze of the recent debate about the origin of the eukaryotic cells; suffice it to say that the picture seems more obscure than 20 y ago. How did eukaryotic life evolve? This is one of the most controversial and puzzling questions in evolutionary history. Life began as single-celled, independent organisms that evolved into cells containing membrane-bound, specialized structures known as organelles. What’s clear is that this new type of cell, the eukaryote, is more complex than its predecessors. What’s unclear is how these changes took place. 24

A.Kauko (2018): The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life.36

F.Rana (2019): The origin of eukaryotes is one of the hardest and most intriguing problems in the study of the evolution of life, and arguably, in the whole of biology. On average, the volume of eukaryotic cells is about 15,000 times larger than that of prokaryotic cells.30

Josip Skejo (2021): Eukaryotic cells are vastly more complex than prokaryotic cells as evident by their endomembrane system 26

A. Spang (2022): Archaea and Bacteria are often referred to as primary domains of life while eukaryotes form a secondary domain of life. The prevalence of horizontal gene transfer (HGT) via both mobile genetic elements (MGEs) and viruses but also directly between distinct organisms has to some extent questioned the concept of a Tree of Life (TOL), which may be more correctly represented as a network including both vertical and horizontal branches.

Arizona State University (2022): The transition from prokaryote to eukaryote has remained a central mystery biologists are still trying to untangle. How this crucial transition came to be remains a central mystery in biology.40

Origin of eukaryotes

M. A. O’Malley (2015):  There are very roughly two main hypotheses for the evolution of eukaryotes: one sees the process as mutation-driven, with lateral acquisitions of genes and organisms also involved but in a causally secondary way; the other sees eukaryogenesis as driven causally by the acquisition of the mitochondrion. The acquisition of the mitochondrion is often portrayed as a one-off event that instigated a rapid transformation with major evolutionary outcomes 38

Eugene V. Koonin (2015): The origin of eukaryotes is one of the hardest and most intriguing problems in the study of the evolution of life, and arguably, in the whole of biology. Compared to archaea and bacteria (collectively, prokaryotes), eukaryotic cells display a qualitatively higher level of complexity of intracellular organization. Unlike the great majority of prokaryotes, eukaryotic cells possess an extended system of intracellular membranes that includes the eponymous eukaryotic organelle, the nucleus, and fully compartmentalizes the intracellular space. In eukaryotic cells, proteins, nucleic acids and small molecules are distributed by specific trafficking mechanisms rather than by free diffusion as is largely the case in bacteria and archaea. Thus, eukaryotic cells function on different physical principles compared to prokaryotic cells, which is directly due to their (comparatively) enormous size. The gulf between the cellular organizations of eukaryotes and prokaryotes is all the more striking because no intermediates have been found. The actin and tubulin cytoskeletons, the nuclear pore, the spliceosome, the proteasome, and the ubiquitin signalling system are only a few of the striking examples of the organizational complexity that seems to be a ‘birthright’ of eukaryotic cells. The formidable problem that these fundamental complex features present to evolutionary biologists makes Darwin’s famous account of the evolution of the eye look like a simple, straightforward case. Indeed, so intimidating is the challenge of eukaryogenesis that the infamous notion of ‘irreducible complexity’ has sneaked into serious scientific debate: 

C. G. Kurland: Genomics and the Irreducible Nature of Eukaryote Cells (2006): Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Because their cells appear simpler, prokaryotes have traditionally been considered ancestors of eukaryotes. Here, we review recent data from proteomics and genome sequences suggesting that eukaryotes are a unique primordial lineage. Mitochondria, mitosomes, and hydrogenosomes are a related family of organelles that distinguish eukaryotes from all prokaryotes. Recent analyses also suggest that early eukaryotes had many introns, and RNAs and proteins found in modern spliceosomes. Nuclei, nucleoli, Golgi apparatus, centrioles, and endoplasmic reticulum are examples of cellular signature structures (CSSs) that distinguish eukaryote cells from archaea and bacteria. Comparative genomics, aided by proteomics of CSSs such as the mitochondria, nucleoli, and spliceosomes, reveals hundreds of proteins with no orthologs  (Orthologs are genes in different species that evolved from a common ancestral gene by speciation) evident in the genomes of prokaryotes; these are the eukaryotic signature proteins (ESPs). The many ESPs within the subcellular structures of eukaryote cells provide landmarks to track the trajectory of eukaryote genomes from their origins. In contrast, hypotheses that attribute eukaryote origins to genome fusion between archaea and bacteria are surprisingly uninformative about the emergence of the cellular and genomic signatures of eukaryotes (CSSs and ESPs). The failure of genome fusion to directly explain any characteristic feature of the eukaryote cell is a critical starting point for studying eukaryote origins. 34